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<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:14.0pt;font-family:"Times New
Roman","serif";
mso-fareast-font-family:"Times New
Roman";mso-ansi-language:EN-US;mso-fareast-language:
FR" lang="EN-US">Sorry, the X and Y were switched in the plot
due to a mishandling. Please
find attached now the correct AED graph. <o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:14.0pt;font-family:"Times New
Roman","serif";
mso-fareast-font-family:"Times New
Roman";mso-ansi-language:EN-US;mso-fareast-language:
FR" lang="EN-US">The round 3 (red curve) shows little higher
overall AED than the second
round (green curve) and more genes (<span
style="color:#212121;background:white">22931
comparing to 22547 in the round 2). Do you think that I
should stop at the
second round ?</span> <o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:14.0pt;font-family:"Times New
Roman","serif";
mso-fareast-font-family:"Times New
Roman";mso-ansi-language:EN-US;mso-fareast-language:
FR" lang="EN-US">I didn't<span style="mso-spacerun:yes"> </span>precise
in the precedent
email that the Repeat masking was done in Maker using the
Repbase and only
models found by RepeatModeler having identities. I let<span
style="mso-spacerun:yes"> </span>unmasked the unkown lib
of RepeatModeler. In
fact we expect a high rate of segmental and gene duplication
in the genome and
then we could explain the high overall count of genes found
by Maker.<o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
line-height:normal"><span
style="font-size:14.0pt;font-family:"Times New
Roman","serif";
mso-fareast-font-family:"Times New
Roman";mso-ansi-language:EN-US;mso-fareast-language:
FR" lang="EN-US">In the other hand the high, rate of genes may
be also expalined by the fact
that I activate the alt_splice=1 option to find alternative
splicing, do you
think that it was a good idea ?<o:p></o:p></span></p>
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<p><span style="mso-ansi-language:EN-US" lang="EN-US">Best,</span>
<p class="MsoNormal">Amine<br>
<span style="mso-ansi-language:EN-US" lang="EN-US"><o:p></o:p></span></p>
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<br>
<div class="moz-cite-prefix">Le 26/10/2016 à 20:06, Carson Holt a
écrit :<br>
</div>
<blockquote
cite="mid:3EA2EC84-9B2A-4631-97F8-44D774E67468@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Sorry. I also assumed X and Y was flipped when I looked at it. Now
I read the labels, your AED curve would be weird unless the X and
Y are flipped in your figure.
<div class=""><br class="">
</div>
<div class="">—Carson</div>
<div class=""><br class="">
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Oct 26, 2016, at 12:04 PM, Carson Holt
<<a moz-do-not-send="true"
href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;"
class="">Your AED curve looks fine. The first run
(using protein2genome or est2genome I assume) will
always have really low overall AED because they are
exact copies of the protein/transcript alignments (so
AED is meaningless there because it will always
artificially look good). The protein2genome or
est2genome modles also have a hard end-to-end coverage
filtering cutoff of 0.5 when generated (apparent in
the curve - value in maker_bopts.ctl). The next runs
with SNAP show >80% of models with AED under 0.5,
so it looks good. You can further look at models by
adding protein domains using InterProScan in which you
would expect 70-80% of models to contain a
recognizable InterPro domain (false and bad models
will result in very low overall domain content).
<div class=""><br class="">
</div>
<div class="">Your overall gene counts are a little
high though for an arthropod (14,000-19,000 genes
would be expected as gene loss rather than gene gain
is the primary evolutionary force in the Ecdysozoa).
However your gene counts can be explained by either
insufficient repeat masking (you can add a
RepeatModeler generated library to the existing
settings to help with this), poor mRNA-seq assembly
or a lot of noise in the RNA-seq (this can be helped
with more strict assembly parameters including the
jaccard-clip option in trinity), or it is just the
result of assembly fragmentation (if you have a lot
of contigs or runs of NNNN in the assembly, then
many genes will be split which results in inflated
gene counts).<br class="">
<div class=""><br class="">
</div>
<div class="">Finally manually look at the most gene
dense contigs in a browser like Apollo or IGV
(gene_density = gene_count / contig_length). If
the most gene dense contigs are overwhelmingly
single exon, then you may need to filter out some
prokaryotic assembly contamination (not uncommon).
If you have contamination, it will assemble as
independent contigs, so is easily blacklisted and
can be identified visually (always gene dense and
single exon).</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Carson</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Oct 26, 2016, at 7:09 AM,
Mohamed Amine Chebbi <<a
moz-do-not-send="true"
href="mailto:mohamed.amine.chebbi@univ-poitiers.fr"
class=""><a class="moz-txt-link-abbreviated" href="mailto:mohamed.amine.chebbi@univ-poitiers.fr">mohamed.amine.chebbi@univ-poitiers.fr</a></a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<div style="font-family: arial, helvetica,
sans-serif; font-size: 12pt;" class="">
<div class="">
<div style="margin: 0px; line-height:
normal;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;
background: white;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;
background: white;" class="">Hi !
</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
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class="">I have tried three rounds
of annotation in Maker on a non
model arthropod genome (1.7Gb)
which is an hybrid assembly of
Pacbio and illumina reads.</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class="">As suggested in the
tutorial, I ran in the first round
Maker with repeat masking to
generate gene models using
transcript (Trinity assembly) and
protein (swissprot) evidence. Then
Maker models were used twice in a
bootstrap fashion to retrain SNAP.
</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class="">The number of genes drops
from </span><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;" class="">29207
in the round 1 to 22547 in the
round 2 then increases slightly to
22931 in the round 3.</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><br class="">
<span style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;" class=""><span style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;" data-mce-style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;" class="">However, the AED profile (attached) don't seem to be satisfactory.</span></span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #212121;
background: white;" class="">So I
wonder if you could let me a good
strategy to improve the annotation
quality. Do you think that
filtering good transcripts could
improve results. If yes , which
criteria should</span><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class=""> be taken into account ?</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class="">Thank you.</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class=""><br data-mce-bogus="1"
class="">
</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class="">Best;</span></div>
<div style="line-height: normal;
background-color: white; margin:
0px; background-position: initial
initial; background-repeat: initial
initial;" class=""><span
style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
data-mce-style="font-size: 12.0pt;
font-family: 'Times New
Roman','serif'; color: #222222;"
class="">Amine</span></div>
</div>
</div>
</div>
<span
id="cid:A35AEA9C-A0B8-490E-84CF-C956A8207A2C@genetics.utah.edu"
class=""><AED-Graph.pdf></span>_______________________________________________<br
class="">
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</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Mohamed Amine CHEBBI, PhD Student
Université de Poitiers
Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267
Equipe Ecologie Evolution Symbiose
Bât. B8-B35 - 5 Rue Albert Turpin
TSA 51106
F-86022 Poitiers Cedex 9
FRANCE
Lab website: <a class="moz-txt-link-freetext" href="http://ecoevol.labo.univ-poitiers.fr/">http://ecoevol.labo.univ-poitiers.fr/</a></pre>
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